segment_juncs v1.0.13
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Loading reference sequences...
	Loading chr1...done
	Loading chr2...done
	Loading chr3...done
	Loading chr4...done
	Loading chr5...done
	Loading chr6...done
	Loading chr7...done
	Loading chr8...done
	Loading chr9...done
	Loading chr10...done
	Loading chr11...done
	Loading chr12...done
	Loading chr13...done
	Loading chr14...done
	Loading chr15...done
	Loading chr16...done
	Loading chr17...done
	Loading chr18...done
	Loading chr19...done
	Loading chr20...done
	Loading chr21...done
	Loading chr22...done
	Loading chrX...done
	Loading chrY...done
	Loading chrM...done
Loading left segment hits...	Processed 500000 root segment groups
Microaligned 0 segments
done.
Loading right segment hits...	Processed 500000 root segment groups
	Processed 1000000 root segment groups
	Processed 1500000 root segment groups
	Processed 2000000 root segment groups
	Processed 2500000 root segment groups
Microaligned 0 segments
done.
Found 3669285 potential split-segment junctions
Indexing extensions in /projects/NBL/HS1195/30TTYAAXX_5/tophat_wj/tmp//left_kept_reads_seg1_missing.fq
Indexing extensions in /projects/NBL/HS1195/30TTYAAXX_5/tophat_wj/tmp//left_kept_reads_seg2_missing.fq
Indexing extensions in /projects/NBL/HS1195/30TTYAAXX_5/tophat_wj/tmp//right_kept_reads_seg1_missing.fq
Indexing extensions in /projects/NBL/HS1195/30TTYAAXX_5/tophat_wj/tmp//right_kept_reads_seg2_missing.fq
Total extensions: 93684976
Total extensions: 93684976
Total extensions: 93684976
Total extensions: 93684976
Looking for junctions by island end pairings
Adding hits from segment file 0 to coverage map
Adding hits from segment file 1 to coverage map
Adding hits from segment file 2 to coverage map
Adding hits from segment file 3 to coverage map
Map covers 102838758 bases
Map covers 100970345 bases in sufficiently long segments
Map contains 1855626 good islands
92456932 are left looking bases
92455141 are right looking bases
Collecting potential splice sites in islands
reporting synthetic splice junctions...
Examining donor-acceptor pairings in chr20
Examining donor-acceptor pairings in chr21
Examining donor-acceptor pairings in chr22
Examining donor-acceptor pairings in chr19
Examining donor-acceptor pairings in chr18
Examining donor-acceptor pairings in chr11
Examining donor-acceptor pairings in chr10
Examining donor-acceptor pairings in chr13
Examining donor-acceptor pairings in chr12
Examining donor-acceptor pairings in chr15
Examining donor-acceptor pairings in chr14
Examining donor-acceptor pairings in chr17
Examining donor-acceptor pairings in chr16
Examining donor-acceptor pairings in chrX
Examining donor-acceptor pairings in chrY
Examining donor-acceptor pairings in chrM
Examining donor-acceptor pairings in chr2
Examining donor-acceptor pairings in chr3
Examining donor-acceptor pairings in chr1
Examining donor-acceptor pairings in chr6
Examining donor-acceptor pairings in chr7
Examining donor-acceptor pairings in chr4
Examining donor-acceptor pairings in chr5
Examining donor-acceptor pairings in chr8
Examining donor-acceptor pairings in chr9
Found 5000000 potential island-end pairing junctions
done
Reporting potential splice junctions...done
Reported 8232613 total possible splices